In order effectively diagnose or treat a subject suffering from a mutation in the subject's gene or from an infection with a pathogen, it is frequently desirable to obtain detailed genetic information relating to the mutation or the pathogen.
For example, methicillin-resistant Staphylococcus aureus (MRSA) is a type of Staphylococcus aureus (S. aureus) which can cause infection in humans and is resistant to beta-lactam antibiotics. As a result of its resistance to certain antibiotics, MRSA infections can be difficult to treat.
S. aureus bacteria typically become methicillin-resistant through acquiring the mecA gene. The mecA gene is typically located in the staphyloccal cassette chromosome mec (SCCmec), which is a multi-gene, transferable genomic element. Different types of SCCmec exist, with known SCCmec types ranging in size from approximately 21,000-67,000 nucleotides in length. Generally, within each type of SCCmec, the mecA gene is surrounded by other genes or elements which are other components of the SCCmec. In MRSA bacteria, SCCmec containing the mecA gene is integrated into the S. aureus chromosome.
In order identify and control MRSA bacteria, effective reagents and methods for MRSA detection are needed. In addition, improved reagents and methods for assessing other integrated genes in host genetic material and also for assessing whether two or more genetic elements are in a common molecule are needed.
As another example, within Hepatitis C genotype 1a, there is a polymorphic site Q80K in the protease gene, nonstructural protein 3 (“NS3”; also known as “p-70”), that is associated with treatment failure with the protease inhibitor boceprevir, which otherwise can be effective in blocking peptide maturation in the virus. Assessing the Q80 polymorphism in the NS3 gene in patients with subtype 1a can be an important part of formulating a treatment plan.
Accordingly, improved reagents and methods for assessing the Q80 polymorphism are needed. In addition, improved reagents and methods for assessing other SNPs, point mutations, and other nucleotide variations are needed.